Bioinformatics Scientist | Computational Biologist

Creative and self-driven scientist with 10+ years of hands-on experience in bioinformatics. Looking for a position that integrates large omics datasets and statistical modeling to uncover novel biological insight.

Ph.D, Biology

University of Virginia

Charlottesville, VA

2018 - 2012

B.S Biology

Susquehanna University

Selinsgrove, PA

2012 - 2008

Post Doctoral Fellow

Children’s Hospital of Philadelphia

Philadelphia, PA

Current - 2019

• Performed integrated analyses of NGS datasets (ATAC-seq, ChIP-seq, RNA- seq, HiC/Promoter Capture C) to answer biological questions in metabolic, neuroscience, and immune relevant traits
• Incorporated functional genomics datasets to implicate potential target genes of disease associated variants (variant to gene)
• Investigated the potential genetic contribution of the hypothalamus in puberty, obesity, sleep, and mood disorders
• Consulted with bench scientists on experimental design to minimize batch effects and ensure experimental validity
• Recruited and trained bioinformatics fellows, staff, and graduate students.
• Published 11 peer reviewed publications

Graduate Researcher

University of Virginia

Charlottesville, VA

2018 - 2012

• Initiated and led research project on the regulation of neural stem cell proliferation and cell death during development.
• Designed custom code to mine public ChIP-seq data and predicted a list of screen candidate genes.
• Initiated a directed screen for genes involved in terminating neural stem cell divisions.
• Developed lab protocol for primary cell culture.
• Published two peer-reviewed papers.

Research Intern

Weis Center for Research, Geisinger

Danville PA

2012 - 2010

• Analyzed miRNA microarray and ChIP-Chip data from patient samples to investigate the pathogenesis of abdominal aortic aneurysms.
• Published four peer-reviewed research articles and presented results at two conferences.

3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk

Cell Metabolism

N/A

2022

• Chun Su, Lin Gao, Catherine L. May, James A. Pippin, Keith Boehm, Michelle Lee M, Chengyang Liu, Matthew C Pahl, Maria L Golson, Ali Naji; HPAP Consortium, Strua FA Grant, Andrew D. Wells, Klaus H. Kaestner

Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture C in disease relevant immune cell types.

Genome Biology

N/A

2022

• Matthew C Pahl, Carol Le Coz, Chun Su, Prabhat Sharma, Rajan M Tomas, Jame A Pippin, EC Caberara, Matthew E Johnson, Michelle Leonard, Sumei Lu, Alessandra Chesi, Katherine E Sullivan, Neil Romberg, Struan FA Grant, Andrew D Wells

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

Nature Communication

N/A

2021

• Matthew C Pahl, Claudia A. Doege, Kenyaita M. Hodge, Sheridan H. Littleton, Michelle E. Leonard, Sumei Lu, Rick Rausch, James A. Pippin, Maria Caterina De Rosa, Alisha Basak, Jonathan P. Bradfield, Reza K. Hammond, Keith Boehm, Robert I. Berkowitz, Chiara Lasconi, Chun Su, Alessandra Chesi, Matthew E. Johnson, Andrew D. Wells, Benjamin F. Voight, Rudolph L. Leibel, Diana L. Cousminer & Struan F. A.

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping.

Genome Biology

N/A

2021

• Diana L Cousminer, Yadav Wagley, James A Pippin, Ahmed Elhakeem, Gregory P Way, Matthew C Pahl, Shana E McCormack, Alessandra Chesi, Jonathan A Mitchell, Joseph M Kindler, Denis Baird, April Hartley, Laura Howe, Heidi J Kalkwarf , Joan M Lappe, Sumei Lu, Michelle Leonard, Matthew E. Johnson, Hakon Hakonarson, Vicente Gilsanz, John A Shepherd, Sharon E Oberiield, Casey S Greene, Andrea Kelly, Deborah A Lawlor, Ben F Voight, Andrew Wells, Babette S Zemel, Kurt D Hankenson, Struan FA Grant

E93 Integrates Neuroblast Intrinsic State with Developmental Time to Terminate MB Neurogenesis via Autophagy.

Current Biology

N/A

2019

• Matthew C Pahl, Susan E Doyle, Sarah E Siegrist

Transcriptional (ChIP-Chip) Analysis of ELF1, ETS2, RUNX1 and STAT5 in Human Abdominal Aortic Aneurysm

Int J Mol Sci

N/A

2015

• Matthew C Pahl, Robert Erdman, Helena Kuivaniemi, John H Lillvis, James R Elmore, Gerard Tromp.

MicroRNA expression signature in human abdominal aortic aneurysms

BMC Medical Genomics

N/A

2012

• Matthew C Pahl, Kimberly Derr, Gabor Gabel, Irene Hinterseher, James R Elmore, Charles M Schworer, Thomas C Peeler, David P Franklin, John L Gray, Gerard Tromp, Helena Kuivaniemi